Just what is a 'drone control subsystem'? What exactly constitutes 'Flood activity'?

Could this have been Cortana? It would be a way to explain how she got the index even though shes "stuck" in the core. Maybe she was the one messing stuff up and making it a pain for the security doors to open. Really you would think 343GS would be able to open his own doors, but instead he keeps having to go do security overrides. Maybe this is cortana trying to stop MC and 343GS from getting to the index. After she sees GS can override even the locked doors then she gets into a drone subsytem and uses a drone (reprogramed or not) to retrieve the index herself. She locks all the doors to slow MS and GS down as much as possible so she has time to retrieve the index herself. Not knowing about cortana 343GS can only assume it's the "flood activity" thats making things go wrong. At this point we can see the covenant aren't in the library, so 343GS thinks it's the flood whos breaking stuff.